Tests

Fix workflow links and update wrapper prefix #35

	name: Tests

	on:
	push:
	branches:
	- main
	pull_request:
	branches_ignore: []

	jobs:
	Linting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	- name: Lint workflow
	uses: snakemake/[email protected]
	with:
	directory: .
	snakefile: workflow/Snakefile
	args: "--lint"

	Testing:
	runs-on: ubuntu-latest
	needs: Linting
	timeout-minutes: 30
	steps:
	- name: Install rsync and mamba
	run: sudo apt-get install -y mamba rsync
	- name: Checkout repository and submodules
	uses: actions/checkout@v2
	with:
	submodules: recursive
	- name: Test workflow (local test data)
	uses: snakemake/[email protected]
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba --wrapper-prefix file:///github/workspace/workflow/wrappers"
	- name: Test report
	uses: snakemake/[email protected]
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--report report.zip --wrapper-prefix file:///github/workspace/workflow/wrappers"

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